pertpy 0.11.1__tar.gz → 0.11.3__tar.gz

{pertpy-0.11.1 → pertpy-0.11.3}/.github/release-drafter.yml

@@ -1,5 +1,5 @@
-name-template: "0.11.1 🌈"
-tag-template: 0.11.1
+name-template: "0.11.3 🌈"
+tag-template: 0.11.3
 exclude-labels:
     - "skip-changelog"
 

{pertpy-0.11.1 → pertpy-0.11.3}/.github/workflows/test.yml

@@ -24,13 +24,8 @@ jobs:
                 include:
                     - os: ubuntu-latest
                       python: "3.13"
-                      run_mode: "slow"
                     - os: ubuntu-latest
                       python: "3.13"
-                      run_mode: "fast"
-                    - os: ubuntu-latest
-                      python: "3.13"
-                      run_mode: slow
                       pip-flags: "--pre"
 
         env:
@@ -91,9 +86,6 @@ jobs:
                   DISPLAY: :42
               run: |
                   pytest_args="-m pytest -v --color=yes"
-                  if [ "${{ matrix.run_mode }}" = "slow" ]; then
-                    pytest_args="$pytest_args --runslow"
-                  fi
                   coverage run $pytest_args
 
             - name: Show coverage report

{pertpy-0.11.1 → pertpy-0.11.3}/.pre-commit-config.yaml

@@ -11,7 +11,7 @@ repos:
       hooks:
           - id: biome-format
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.11.5
+      rev: v0.11.9
       hooks:
           - id: ruff
             args: [--fix, --exit-non-zero-on-fix, --unsafe-fixes]
@@ -33,7 +33,7 @@ repos:
           - id: no-commit-to-branch
             args: ["--branch=main"]
     - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v1.14.1
+      rev: v1.15.0
       hooks:
           - id: mypy
             args: [--no-strict-optional, --ignore-missing-imports]

{pertpy-0.11.1 → pertpy-0.11.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pertpy
-Version: 0.11.1
+Version: 0.11.3
 Summary: Perturbation Analysis in the scverse ecosystem.
 Project-URL: Documentation, https://pertpy.readthedocs.io
 Project-URL: Source, https://github.com/scverse/pertpy
@@ -132,26 +132,54 @@ You can install _pertpy_ in less than a minute via [pip] from [PyPI]:
 pip install pertpy
 ```
 
+### Differential gene expression
+
+If you want to use the differential gene expression interface, please install pertpy by running:
+
+```console
+pip install 'pertpy[de]'
+```
+
+### tascCODA
+
 if you want to use tascCODA, please install pertpy as follows:
 
 ```console
 pip install 'pertpy[tcoda]'
 ```
 
-If you want to use the differential gene expression interface, please install pertpy by running:
+### milo
+
+milo further requires edger, statmod, and rpy2 to be installed:
+
+```R
+BiocManager::install("edgeR")
+BiocManager::install("statmod")
+```
 
 ```console
-pip install 'pertpy[de]'
+pip install rpy2
 ```
 
 ## Citation
 
-[Lukas Heumos, Yuge Ji, Lilly May, Tessa Green, Xinyue Zhang, Xichen Wu, Johannes Ostner, Stefan Peidli, Antonia Schumacher, Karin Hrovatin, Michaela Mueller, Faye Chong, Gregor Sturm, Alejandro Tejada, Emma Dann, Mingze Dong, Mojtaba Bahrami, Ilan Gold, Sergei Rybakov, Altana Namsaraeva, Amir Ali Moinfar, Zihe Zheng, Eljas Roellin, Isra Mekki, Chris Sander, Mohammad Lotfollahi, Herbert B. Schiller, Fabian J. Theis
-bioRxiv 2024.08.04.606516; doi: https://doi.org/10.1101/2024.08.04.606516](https://www.biorxiv.org/content/10.1101/2024.08.04.606516v1)
+```bibtex
+@article {Heumos2024.08.04.606516,
+    author = {Heumos, Lukas and Ji, Yuge and May, Lilly and Green, Tessa and Zhang, Xinyue and Wu, Xichen and Ostner, Johannes and Peidli, Stefan and Schumacher, Antonia and Hrovatin, Karin and Müller, Michaela and Chong, Faye and Sturm, Gregor and Tejada, Alejandro and Dann, Emma and Dong, Mingze and Bahrami, Mojtaba and Gold, Ilan and Rybakov, Sergei and Namsaraeva, Altana and Moinfar, Amir and Zheng, Zihe and Roellin, Eljas and Mekki, Isra and Sander, Chris and Lotfollahi, Mohammad and Schiller, Herbert B. and Theis, Fabian J.},
+    title = {Pertpy: an end-to-end framework for perturbation analysis},
+    elocation-id = {2024.08.04.606516},
+    year = {2024},
+    doi = {10.1101/2024.08.04.606516},
+    publisher = {Cold Spring Harbor Laboratory},
+    URL = {https://www.biorxiv.org/content/early/2024/08/07/2024.08.04.606516},
+    eprint = {https://www.biorxiv.org/content/early/2024/08/07/2024.08.04.606516.full.pdf},
+    journal = {bioRxiv}
+}
+```
 
 [pip]: https://pip.pypa.io/
 [pypi]: https://pypi.org/
-[api]: https://pertpy.readthedocs.io/en/latest/api/api.html
+[api]: https://pertpy.readthedocs.io/en/latest/api.html
 [//]: # "numfocus-fiscal-sponsor-attribution"
 
 pertpy is part of the scverse® project ([website](https://scverse.org), [governance](https://scverse.org/about/roles)) and is fiscally sponsored by [NumFOCUS](https://numfocus.org/).

{pertpy-0.11.1 → pertpy-0.11.3}/README.md

@@ -29,26 +29,54 @@ You can install _pertpy_ in less than a minute via [pip] from [PyPI]:
 pip install pertpy
 ```
 
+### Differential gene expression
+
+If you want to use the differential gene expression interface, please install pertpy by running:
+
+```console
+pip install 'pertpy[de]'
+```
+
+### tascCODA
+
 if you want to use tascCODA, please install pertpy as follows:
 
 ```console
 pip install 'pertpy[tcoda]'
 ```
 
-If you want to use the differential gene expression interface, please install pertpy by running:
+### milo
+
+milo further requires edger, statmod, and rpy2 to be installed:
+
+```R
+BiocManager::install("edgeR")
+BiocManager::install("statmod")
+```
 
 ```console
-pip install 'pertpy[de]'
+pip install rpy2
 ```
 
 ## Citation
 
-[Lukas Heumos, Yuge Ji, Lilly May, Tessa Green, Xinyue Zhang, Xichen Wu, Johannes Ostner, Stefan Peidli, Antonia Schumacher, Karin Hrovatin, Michaela Mueller, Faye Chong, Gregor Sturm, Alejandro Tejada, Emma Dann, Mingze Dong, Mojtaba Bahrami, Ilan Gold, Sergei Rybakov, Altana Namsaraeva, Amir Ali Moinfar, Zihe Zheng, Eljas Roellin, Isra Mekki, Chris Sander, Mohammad Lotfollahi, Herbert B. Schiller, Fabian J. Theis
-bioRxiv 2024.08.04.606516; doi: https://doi.org/10.1101/2024.08.04.606516](https://www.biorxiv.org/content/10.1101/2024.08.04.606516v1)
+```bibtex
+@article {Heumos2024.08.04.606516,
+    author = {Heumos, Lukas and Ji, Yuge and May, Lilly and Green, Tessa and Zhang, Xinyue and Wu, Xichen and Ostner, Johannes and Peidli, Stefan and Schumacher, Antonia and Hrovatin, Karin and Müller, Michaela and Chong, Faye and Sturm, Gregor and Tejada, Alejandro and Dann, Emma and Dong, Mingze and Bahrami, Mojtaba and Gold, Ilan and Rybakov, Sergei and Namsaraeva, Altana and Moinfar, Amir and Zheng, Zihe and Roellin, Eljas and Mekki, Isra and Sander, Chris and Lotfollahi, Mohammad and Schiller, Herbert B. and Theis, Fabian J.},
+    title = {Pertpy: an end-to-end framework for perturbation analysis},
+    elocation-id = {2024.08.04.606516},
+    year = {2024},
+    doi = {10.1101/2024.08.04.606516},
+    publisher = {Cold Spring Harbor Laboratory},
+    URL = {https://www.biorxiv.org/content/early/2024/08/07/2024.08.04.606516},
+    eprint = {https://www.biorxiv.org/content/early/2024/08/07/2024.08.04.606516.full.pdf},
+    journal = {bioRxiv}
+}
+```
 
 [pip]: https://pip.pypa.io/
 [pypi]: https://pypi.org/
-[api]: https://pertpy.readthedocs.io/en/latest/api/api.html
+[api]: https://pertpy.readthedocs.io/en/latest/api.html
 [//]: # "numfocus-fiscal-sponsor-attribution"
 
 pertpy is part of the scverse® project ([website](https://scverse.org), [governance](https://scverse.org/about/roles)) and is fiscally sponsored by [NumFOCUS](https://numfocus.org/).

{pertpy-0.11.1 → pertpy-0.11.3}/docs/_static/pertpy_logo.svg

@@ -1,5 +1,4 @@
 <svg width="308" height="105" viewBox="0 0 308 105" fill="none" xmlns="http://www.w3.org/2000/svg">
-<rect width="308" height="105" fill="#1E1E1E"/>
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 </svg>

pertpy-0.11.3/docs/about/background.md

@@ -0,0 +1,49 @@
+# About Pertpy
+
+Pertpy is an end-to-end framework for the analysis of large-scale single-cell perturbation experiments.
+It provides access to harmonized perturbation datasets and metadata databases along with numerous fast and user-friendly implementations of both established and novel methods such as automatic metadata annotation or perturbation distances to efficiently analyze perturbation data.
+As part of the scverse ecosystem, pertpy interoperates with existing single-cell analysis libraries and is designed to be easily extended.
+If you find pertpy useful for your research, please check out {doc}`cite`.
+
+## Design principles
+
+Our framework is based on three key principles: `Modularity`, `Flexibility`, and `Scalability`.
+
+### Modularity
+
+Pertpy includes modules for analysis of single and combinatorial perturbations covering diverse types of perturbation data including genetic knockouts, drug screens, and disease states.
+The framework is designed for flexibility, offering more than 100 composable and interoperable analysis functions organized in modules which further ease downstream interpretation and visualization.
+These modules host fundamental building blocks for implementation and methods that share functionality and can be chained into custom pipelines.
+
+A typical Pertpy workflow consists of several steps:
+
+* Initial **data transformation** such as guide RNA assignment for CRISPR screens
+* **Quality control** to address confounding factors and technical variation
+* **Metadata annotation** against ontologies and enrichment from databases
+* **Perturbation space analysis** to learn biologically interpretable embeddings
+* **Downstream analysis** including differential expression, compositional analysis, and distance calculation
+
+This modular approach yields a powerful and flexible framework as many analysis steps can be independently applied or chained together.
+
+### Flexibility
+
+Pertpy is purpose-built to organize, analyze, and visualize complex perturbation datasets.
+It is flexible and can be applied to datasets of different assays, data types, sizes, and perturbations, thereby unifying previous data-type- or assay-specific single-problem approaches.
+Designed to integrate external metadata with measured data, it enables unprecedented contextualization of results through swiftly built, experiment-specific pipelines, leading to more robust outcomes.
+
+The inputs to a typical analysis with pertpy are unimodal scRNA-seq or multimodal perturbation readouts stored in AnnData or MuData objects.
+While pertpy is primarily designed to explore perturbations such as genetic modifications, drug treatments, exposure to pathogens, and other environmental conditions, its utility extends to various other perturbation settings, including diverse disease states where experimental perturbations have not been applied.
+
+### Scalability
+
+Pertpy addresses a wide array of use-cases and different types of growing datasets through its sparse and memory-efficient implementations, which leverage the parallelization and GPU acceleration library Jax, and numba, thereby making them substantially faster than original implementations.
+The framework can be applied to datasets ranging from thousands to millions of cells.
+
+For example, when analyzing CRISPR screens, Pertpy's implementation of Mixscape is optimized using PyNNDescent for nearest neighbor search during the calculation of perturbation signatures.
+Other methods such as scCODA and tascCODA are accelerated by replacing the Hamiltonian Monte Carlo algorithm in TensorFlow with the no-U-turn sampler from numpyro.
+CINEMA-OT is optimized with ott-jax to make the implementation portable across hardware, enabling GPU acceleration.
+
+## Why is it called "Pertpy"?
+
+Pertpy is named for its core purpose: The analysis of **pert**urbations in **Py**thon.
+The framework unifies perturbation analysis approaches across different data types and experimental designs, providing a comprehensive solution for understanding cellular responses to various stimuli.

pertpy-0.11.3/docs/about/cite.md

@@ -0,0 +1,20 @@
+# Citing pertpy
+
+If you find pertpy useful for your research, please consider citing our work as follows:
+
+```bibtex
+@article {Heumos2024.08.04.606516,
+    author = {Heumos, Lukas and Ji, Yuge and May, Lilly and Green, Tessa and Zhang, Xinyue and Wu, Xichen and Ostner, Johannes and Peidli, Stefan and Schumacher, Antonia and Hrovatin, Karin and Müller, Michaela and Chong, Faye and Sturm, Gregor and Tejada, Alejandro and Dann, Emma and Dong, Mingze and Bahrami, Mojtaba and Gold, Ilan and Rybakov, Sergei and Namsaraeva, Altana and Moinfar, Amir and Zheng, Zihe and Roellin, Eljas and Mekki, Isra and Sander, Chris and Lotfollahi, Mohammad and Schiller, Herbert B. and Theis, Fabian J.},
+    title = {Pertpy: an end-to-end framework for perturbation analysis},
+    elocation-id = {2024.08.04.606516},
+    year = {2024},
+    doi = {10.1101/2024.08.04.606516},
+    publisher = {Cold Spring Harbor Laboratory},
+    URL = {https://www.biorxiv.org/content/early/2024/08/07/2024.08.04.606516},
+    eprint = {https://www.biorxiv.org/content/early/2024/08/07/2024.08.04.606516.full.pdf},
+    journal = {bioRxiv}
+}
+```
+
+If you are using any previously published tool, please also cite the original publication.
+All tool specific references can be found here: {doc}`../references`.

{pertpy-0.11.1 → pertpy-0.11.3}/docs/changelog.md

@@ -5,6 +5,20 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## v0.11.3
+
+## 🚀 Features
+
+* add about page (#770) @Zethson
+* Simplify Metadata errors (#765) @Zethson
+* Standardize scCODA plot palette interface (#773) @mschilli87
+
+## v0.11.2
+
+### 🚀 Features
+
+* Simplify Metadata errors ([#765](https://github.com/scverse/pertpy/pull/765)) @Zethson
+
 ## v0.11.1
 
 ### 🐛 Bug Fixes

{pertpy-0.11.1 → pertpy-0.11.3}/docs/conf.py

@@ -128,6 +128,7 @@ nitpick_ignore = [
     ("py:class", "pertpy.tools._distances._distances.MeanVar"),
     ("py:class", "The requested data as a NumPy array."),
     ("py:class", "The full registry saved with the model"),
+    ("py:class", "The requested data."),
     ("py:class", "Model with loaded state dictionaries."),
     ("py:class", "pertpy.tools.lazy_import.<locals>.Placeholder"),
 ]

{pertpy-0.11.1 → pertpy-0.11.3}/docs/index.md

@@ -46,7 +46,7 @@ It provides tools for harmonizing perturbation datasets, automating metadata ann
 ```
 
 ```{toctree}
-:caption: 'General:'
+:caption: 'General'
 :hidden: true
 :maxdepth: 1
 
@@ -58,7 +58,7 @@ references
 ```
 
 ```{toctree}
-:caption: 'Gallery:'
+:caption: 'Gallery'
 :hidden: true
 :maxdepth: 1
 
@@ -66,10 +66,32 @@ tutorials
 usecases
 ```
 
+```{toctree}
+:caption: 'About'
+:hidden: true
+:maxdepth: 1
+
+about/background
+about/cite
+GitHub <https://github.com/scverse/pertpy>
+Discourse <https://discourse.scverse.org/c/ecosystem/pertpy/46>
+```
+
 ## Citation
 
-[Lukas Heumos, Yuge Ji, Lilly May, Tessa Green, Xinyue Zhang, Xichen Wu, Johannes Ostner, Stefan Peidli, Antonia Schumacher, Karin Hrovatin, Michaela Mueller, Faye Chong, Gregor Sturm, Alejandro Tejada, Emma Dann, Mingze Dong, Mojtaba Bahrami, Ilan Gold, Sergei Rybakov, Altana Namsaraeva, Amir Ali Moinfar, Zihe Zheng, Eljas Roellin, Isra Mekki, Chris Sander, Mohammad Lotfollahi, Herbert B. Schiller, Fabian J. Theis
-bioRxiv 2024.08.04.606516; doi: https://doi.org/10.1101/2024.08.04.606516](https://www.biorxiv.org/content/10.1101/2024.08.04.606516v1)
+```bibtex
+@article {Heumos2024.08.04.606516,
+    author = {Heumos, Lukas and Ji, Yuge and May, Lilly and Green, Tessa and Zhang, Xinyue and Wu, Xichen and Ostner, Johannes and Peidli, Stefan and Schumacher, Antonia and Hrovatin, Karin and Müller, Michaela and Chong, Faye and Sturm, Gregor and Tejada, Alejandro and Dann, Emma and Dong, Mingze and Bahrami, Mojtaba and Gold, Ilan and Rybakov, Sergei and Namsaraeva, Altana and Moinfar, Amir and Zheng, Zihe and Roellin, Eljas and Mekki, Isra and Sander, Chris and Lotfollahi, Mohammad and Schiller, Herbert B. and Theis, Fabian J.},
+    title = {Pertpy: an end-to-end framework for perturbation analysis},
+    elocation-id = {2024.08.04.606516},
+    year = {2024},
+    doi = {10.1101/2024.08.04.606516},
+    publisher = {Cold Spring Harbor Laboratory},
+    URL = {https://www.biorxiv.org/content/early/2024/08/07/2024.08.04.606516},
+    eprint = {https://www.biorxiv.org/content/early/2024/08/07/2024.08.04.606516.full.pdf},
+    journal = {bioRxiv}
+}
+```
 
 ## NumFOCUS
 

{pertpy-0.11.1 → pertpy-0.11.3}/docs/installation.md

@@ -16,17 +16,9 @@ This is the preferred method to install pertpy, as it will always install the mo
 
 If you don't have [pip] installed, this [Python installation guide] can guide you through the process.
 
-## Additional dependency groups
+### Additional dependency groups
 
-### scCODA and tascCODA
-
-TascCODA requires an additional set of dependencies (ete4, pyqt6, and toytree) that can be installed by running:
-
-```console
-pip install pertpy[tcoda]
-```
-
-## Differential gene expression interface
+#### Differential gene expression interface
 
 The DGE interface of pertpy requires additional dependencies that can be installed by running:
 
@@ -44,21 +36,25 @@ BiocManager::install("edgeR")
 pip install rpy2
 ```
 
-## From sources
+#### milo
 
-The sources for pertpy can be downloaded from the [Github repo].
-Please note that you require [poetry] to be installed.
+milo further requires edger, statmod, and rpy2 to be installed:
 
-You can either clone the public repository:
+```R
+BiocManager::install("edgeR")
+BiocManager::install("statmod")
+```
 
 ```console
-$ git clone git://github.com/scverse/pertpy
+pip install rpy2
 ```
 
-Or download the [tarball]:
+#### tascCODA
+
+TascCODA requires an additional set of dependencies (ete4, pyqt6, and toytree) that can be installed by running:
 
 ```console
-$ curl -OJL https://github.com/scverse/pertpy/tarball/master
+pip install pertpy[tcoda]
 ```
 
 ## Apple Silicon
@@ -100,6 +96,22 @@ Follow these steps to install pertpy on an Apple Silicon machine (tested on a Ma
 
 Now you're ready to use pertpy as usual within the environment (`import pertpy`).
 
+## From sources
+
+The sources for pertpy can be downloaded from the [Github repo].
+
+You can either clone the public repository:
+
+```console
+$ git clone git://github.com/scverse/pertpy
+```
+
+Or download the [tarball]:
+
+```console
+$ curl -OJL https://github.com/scverse/pertpy/tarball/master
+```
+
 [github repo]: https://github.com/scverse/pertpy
 [pip]: https://pip.pypa.io
 [poetry]: https://python-poetry.org/

{pertpy-0.11.1 → pertpy-0.11.3}/pertpy/__init__.py

@@ -2,7 +2,7 @@
 
 __author__ = "Lukas Heumos"
 __email__ = "lukas.heumos@posteo.net"
-__version__ = "0.11.1"
+__version__ = "0.11.3"
 
 import warnings
 

{pertpy-0.11.1 → pertpy-0.11.3}/pertpy/data/_dataloader.py

@@ -15,8 +15,8 @@ from rich.progress import Progress
 
 def _download(  # pragma: no cover
     url: str,
-    output_file_name: str = None,
-    output_path: str | Path = None,
+    output_file_name: str | None = None,
+    output_path: str | Path | None = None,
     block_size: int = 1024,
     overwrite: bool = False,
     is_zip: bool = False,

{pertpy-0.11.1 → pertpy-0.11.3}/pertpy/metadata/_cell_line.py

@@ -215,7 +215,7 @@ class CellLine(MetaData):
         For each cell, we fetch cell line annotation from either the Dependency Map (DepMap) or The Genomics of Drug Sensitivity in Cancer Project (Cancerxgene).
 
         Args:
-            adata: The data object to annotate.
+            adata: The AnnData object to annotate.
             query_id: The column of ``.obs`` with cell line information.
             reference_id: The type of cell line identifier in the metadata, e.g. ModelID, CellLineName	or StrippedCellLineName.
                           If fetching cell line metadata from Cancerrxgene, it is recommended to choose "stripped_cell_line_name".
@@ -311,11 +311,9 @@ class CellLine(MetaData):
 
         else:
             raise ValueError(
-                f"The requested cell line type {reference_id} is currently unavailable in the database.\n"
-                "Refer to the available reference identifier in the chosen database.\n"
-                "DepMap_ID is compared by default.\n"
-                "Alternatively, create a `CellLineMetaData.lookup()` object to "
-                "obtain the available reference identifiers in the metadata."
+                f"The requested cell line type {reference_id} is unavailable."
+                "Refer to the available reference identifier in the chosen database."
+                "Alternatively, create a `CellLineMetaData.lookup()` object to obtain the available reference identifiers in the metadata."
             )
 
         return adata
@@ -362,11 +360,9 @@ class CellLine(MetaData):
         # then we can compare these keys and fetch the corresponding metadata.
         if query_id not in adata.obs.columns and query_id is not None:
             raise ValueError(
-                f"The specified `query_id` {query_id} can't be found in the `adata.obs`. \n"
-                "Ensure that you are using one of the available query IDs present in the adata.obs for the annotation."
-                "If the desired query ID is not available, you can fetch the cell line metadata "
-                "using the `annotate()` function before calling 'annotate_bulk_rna()'. "
-                "This ensures that the required query ID is included in your data, e.g. stripped_cell_line_name, DepMap ID."
+                f"Specified `query_id` {query_id} can't be found in `adata.obs`. \n"
+                "If the desired query ID is not available, fetch the cell line metadata "
+                "using the `annotate()` function before calling 'annotate_bulk_rna()'."
             )
         if query_id is None:
             query_id = "cell_line_name" if cell_line_source == "sanger" else "DepMap_ID"
@@ -376,9 +372,8 @@ class CellLine(MetaData):
         if cell_line_source == "sanger":
             if query_id not in adata.obs.columns:
                 raise ValueError(
-                    "To annotate bulk RNA data from Wellcome Sanger Institute, `cell_line_name` is used as default reference and query identifier if no `query_id` is given."
-                    "Ensure that you have column `cell_line_name` in `adata.obs` or specify column name in which cell line name is stored."
-                    "If cell line name isn't available in 'adata.obs', use `annotate()` to annotate the cell line first."
+                    f"Missing '{query_id}' in `adata.obs`. For Sanger, need `cell_line_name` column "
+                    f"or specify column with cell line names via `query_id` parameter."
                 )
             if self.bulk_rna_sanger is None:
                 self._download_bulk_rna(cell_line_source="sanger")
@@ -387,9 +382,8 @@ class CellLine(MetaData):
         else:
             if query_id not in adata.obs.columns:
                 raise ValueError(
-                    "To annotate bulk RNA data from Broad Institue, `DepMap_ID` is used as default reference and query identifier if no `query_id` is given."
-                    "Ensure that you have column `DepMap_ID` in `adata.obs` or specify column name in which DepMap ID is stored."
-                    "If DepMap ID isn't available in 'adata.obs', use `annotate()` to annotate the cell line first."
+                    f"Missing '{query_id}' in `adata.obs`. For Broad Institute data, need `DepMap_ID` column "
+                    f"or specify column with DepMap IDs via `query_id` parameter."
                 )
             reference_id = "DepMap_ID"
 
@@ -472,19 +466,16 @@ class CellLine(MetaData):
         # then we can compare these keys and fetch the corresponding metadata.
         if query_id not in adata.obs.columns:
             raise ValueError(
-                f"The specified `query_id` {query_id} can't be found in `adata.obs`. \n"
-                "If the desired query ID is not available, you can fetch the cell line metadata \n"
-                "using the `annotate()` function before calling annotate_protein_expression(). \n"
-                "This ensures that the required query ID is included in your data."
+                f"The specified `query_id` `{query_id}` not found in `adata.obs`. "
+                "Fetch cell line metadata with `annotate()` before calling `annotate_protein_expression()`."
             )
         # Lazily download the proteomics data
         if self.proteomics is None:
             self._download_proteomics()
         if reference_id not in self.proteomics.columns:
             raise ValueError(
-                f"The specified `reference_id`{reference_id} can't be found in the protein expression data. \n"
-                "To solve the issue, please use the reference identifier available in the metadata.  \n"
-                "Alternatively, create a `CellLineMetaData.lookup()` object to obtain the available reference identifiers in the metadata."
+                f"Specified `reference_id` `{reference_id}` not found in protein expression data. "
+                f"Use available reference identifiers in metadata or create `CellLineMetaData.lookup()` object."
             )
 
         identifier_num_all = len(adata.obs[query_id].unique())
@@ -551,11 +542,8 @@ class CellLine(MetaData):
             adata = adata.copy()
         if query_id not in adata.obs.columns:
             raise ValueError(
-                f"The specified `query_id` {query_id} can't be found in the `adata.obs`. \n"
-                "Ensure that you are using one of the available query IDs present in 'adata.obs' for the annotation.\n"
-                "If the desired query ID is not available, you can fetch the cell line metadata "
-                "using the `annotate()` function before calling `annotate_from_gdsc()`. "
-                "This ensures that the required query ID is included in your data."
+                f"Specified `query_id` `{query_id}` not found in `adata.obs`. "
+                "Use an available ID or fetch cell line metadata with `annotate()` before calling `annotate_from_gdsc()`."
             )
         # Lazily download the GDSC data
         if gdsc_dataset == "gdsc_1":
@@ -626,11 +614,8 @@ class CellLine(MetaData):
             adata = adata.copy()
         if query_id not in adata.obs.columns:
             raise ValueError(
-                f"The specified `query_id` {query_id} can't be found in the `adata.obs`. \n"
-                "Ensure that you are using one of the available query IDs present in 'adata.obs' for the annotation.\n"
-                "If the desired query ID is not available, you can fetch the cell line metadata "
-                "using the `annotate()` function before calling `annotate_from_prism()`. "
-                "This ensures that the required query ID is included in your data."
+                f"Specified `query_id` `{query_id}` not found in `adata.obs`. "
+                "Use an available ID or fetch cell line metadata with `annotate()` before calling `annotate_from_prism()`."
             )
         if self.drug_response_prism is None:
             self._download_prism()
@@ -700,7 +685,6 @@ class CellLine(MetaData):
         if self.drug_response_prism is None:
             self._download_prism()
 
-        # Transfer the data
         return LookUp(
             type="cell_line",
             transfer_metadata=[
@@ -775,7 +759,7 @@ class CellLine(MetaData):
             and sum(adata.obsm[metadata_key].columns != adata.var.index.values) > 0
         ):
             raise ValueError(
-                "Column name of metadata is not the same as the index of adata.var. Ensure that the genes are in the same order."
+                "Column name of metadata is not the same as the index of `adata.var`. Ensure that the genes are in the same order."
             )
 
         # Divide cell lines into those are present and not present in the metadata
@@ -832,7 +816,7 @@ class CellLine(MetaData):
         """
         if corr is None or pval is None:
             raise ValueError(
-                "Missing required input parameter: 'corr' or 'pval'. Please call the function `pt.md.CellLine.correlate()` to generate these outputs before proceeding."
+                "Missing required input parameter: 'corr' or 'pval'. Call `pt.md.CellLine.correlate()` before proceeding."
             )
 
         if category == "cell line":

{pertpy-0.11.1 → pertpy-0.11.3}/pertpy/metadata/_compound.py

@@ -3,7 +3,6 @@ from __future__ import annotations
 from typing import TYPE_CHECKING, Literal
 
 import pandas as pd
-import pubchempy as pcp
 
 from ._look_up import LookUp
 from ._metadata import MetaData
@@ -44,6 +43,8 @@ class Compound(MetaData):
         if query_id not in adata.obs.columns:
             raise ValueError(f"The requested query_id {query_id} is not in `adata.obs`.\n Please check again.")
 
+        import pubchempy as pcp
+
         query_dict = {}
         not_matched_identifiers = []
         for compound in adata.obs[query_id].dropna().astype(str).unique():

{pertpy-0.11.1 → pertpy-0.11.3}/pertpy/metadata/_look_up.py

@@ -27,7 +27,7 @@ class LookUp:
         Args:
             type: Metadata type for annotation. One of 'cell_line', 'compound', 'moa' or 'drug.
             transfer_metadata: DataFrames used to generate Lookup object.
-                           This is currently set to None for CompoundMetaData which does not require any dataframes for transfer.
+                Currently set to None for CompoundMetaData which does not require any DataFrames for transfer.
         """
         self.type = type
         if type == "cell_line":

{pertpy-0.11.1 → pertpy-0.11.3}/pertpy/metadata/_metadata.py

@@ -49,11 +49,8 @@ class MetaData:
             if metadata_type in ["protein expression", "bulk RNA", "drug response"]:
                 hint = "Additionally, call the `CellLineMetaData.annotate()` function to acquire more possible query IDs that can be used for cell line annotation purposes."
             raise ValueError(
-                f"Attempting to match the query id {query_id} in 'adata.obs' to the reference id {reference_id} in the metadata.\n"
-                "However, none of the query IDs could be found in the {metadata_type} annotation data.\n"
-                "To resolve this issue, call the `lookup()` function to create a LookUp object.\n"
-                "This enables obtaining the count of matched identifiers in the AnnData object for different types of reference and query IDs.\n"
-                f"{hint}"
+                f"No matches between `{query_id}` in adata.obs and `{reference_id}` in {metadata_type} data. "
+                f"Use `lookup()` to check compatible identifier types. {hint}"
             )
         if len(unmatched_identifiers) == 0:
             return
@@ -61,10 +58,8 @@ class MetaData:
             verbosity = min(verbosity, len(unmatched_identifiers))
             if verbosity > 0:
                 logger.info(
-                    f"There are {total_identifiers} identifiers in `adata.obs`."
-                    f"However, {len(unmatched_identifiers)} identifiers can't be found in the {metadata_type} annotation, "
-                    "leading to the presence of NA values for their respective metadata.\n"
-                    f"Please check again: *unmatched_identifiers[:verbosity]..."
+                    f"{total_identifiers} identifiers in `adata.obs`, {len(unmatched_identifiers)} not found in {metadata_type} data. "
+                    f"NA values present. Unmatched: {unmatched_identifiers[:verbosity]}"
                 )
         else:
             raise ValueError("Only 'all' or a non-negative value is accepted.")